Build a Time Tree via Neighbor-Joining — build

Constructs a phylogenetic time tree from an outbreak matrix by calculating pairwise transmission distances and applying the Neighbor-Joining algorithm.

Usage

build_timetree(outbreak, root = 1, plot = FALSE, ...)

Arguments

outbreak: A data frame with 'id', 'parent_id', 'infection_time', and 'removal_time'.
root: Integer or Character. The ID of the node to use as the root (usually the index case).
plot: Logical. If TRUE, plots the resulting phylogeny.
...: Additional arguments passed to ape::plot.phylo.

Value

An object of class phylo (invisibly).